This is how The Thunderwing timeline goes in My Little Pony Transformers Prime: The Cutie Re-Mark.
[Twilight, Spike, Optimus, and Starlight arrive in the Everfree Forest]
Starlight Glimmer: The Everfree Forest?
Optimus Prime: Well, that is strange.
Spike: Very strange.
Twilight Sparkle: Why would the map bring us here?
[Suddenly, Timber Wolves appear and attack them]
Twilight Sparkle: Timber Wolves!
Spike: What do we do?
Optimus Prime: [bring out his gun] You run, I'll hold them off.
Starlight Glimmer: Okay.
[Twilight, Spike, and Starlight run while Optimus fights the Timber Wolves]
[Optimus manages to fight them off]
Starlight Glimmer: Whoa. That was fast.
Optimus Prime: I told you.
Spike: Wait. Hold on, guys.
Twilight Sparkle: What is it, Spike?
[They see a castle in the distance]
Twilight Sparkle: Whoa.
Optimus Prime: Since when the Princesses referbish their castle?
Starlight Glimmer: I don't know.
[They head over to it]
[They open the door and find the hallway is abandoned]
Starlight Glimmer: Who would decorate the castle so beautifully and just leave it?
Optimus Prime: I do not know.
Spike: Nor do I.
Twilight Sparkle: Hey, look. There's Rarity.
[They see Rarity doing some dusting]
Starlight Glimmer: We came here through time travel.
Optimus Prime: Pursuing her brother.
Spike: He's trying to alter the past.
Twilight Sparkle: And we're trying to stop him.
Thunderwing: Time travel?
[They look up and see Thunderwing sitting on his throne]
Thunderwing: Now that's something I like to see.
[He flies down]
Thunderwing: Tell me how you came by this magic to travel through time.
[They look at each other and nod]
Twilight Sparkle: Well, you see.
Spike: Somepony used it.
Optimus Prime: And we are trying to get it back.
Starlight Glimmer: Before he transforms the space time continuem.
Thunderwing: Nobody in my kingdom but me should possess a magic powerful enough to change time.
Spike: Your kingdom?
Thunderwing: Who else?
Spike: Princess Luna and Princess Celestia.
Twilight Sparkle: What?!
Optimus Prime: What?!
Starlight Glimmer: What?!
Thunderwing: Now, reveal the source of this time magic to me.
Twilight Sparkle: We can take you to it, but you'll have to get past the Timber Wolves.
Starlight Glimmer: She's right.
Thunderwing: I am the ruler of all of Equestria. Do you think I can't deal with Timber Wolves?
Twilight Sparkle: No. We know you can.
Starlight Glimmer: Just try to be tempted to much.
Thunderwing: And if you were thinking of trying to escape....[he chains up Spike and Optimus]...it would be very unfortunate for your friends.
[Later, they head for the Cutie Map, Thunderwing blasting a Timber Wolf out of their way as they walk]
Thunderwing: How does it work?
Twilight Sparkle: A pony from our time used this spell to travel back and change the past.
Starlight Glimmer: And that pony is my brother.
Thunderwing: And now you will give this spell to me! With it, I will ensure that the Elements of Harmony are never found and my reign lasts forever!
Twilight Sparkle: No it won't!
Starlight Glimmer: Forget it!
Twilight Sparkle: We don't have it.
Starlight Glimmer: If you want it, you'll have to ask the pony who has it.
Thunderwing: Very well.
[Thunderwing attacks Starlight and Twilight frees Optimus and Spike]
[A guard bot shows up and it's about to attack when Optimus pounces on it, knocking off its helmet, revealing the face of Arcee]